Dear Amber users/developers,
I am have tried to speed up my simulations by switching from a periodic
system with PME to a non-periodic system with a cap of ~300 water
molecules on a ligand binding site. My goal is to calculate relative
ligand binding energies with MM-PBSA and TI.
I first used a non bonded cutoff of 12A for the non-periodic system.
This lead to fluctuations of ~1000 to 2000 kcal/mol of the electrostatic
energy (corresponding to 10% of the total energy) preventing equilibration.
Using a cutoff larger than my system and switching off the update of the
non-bonded pairlist solved this problem - but now the simulations are
significantly slower than for the periodic system (details below).
Is this to be expected?
Do I miss something that could speed up the simulations with the cap
without leading to instability of the electrostatic energy?
Some more details:
I am using sander of AMBER8.
Periodic system:
size: 50000 atoms, truncated octahedron, cut=8A
performance: 80ps/day (with dt=0.002)
non-periodic system:
size: 10000 atoms
performance: 30ps/day (dt=0.002)
The input for the non-periodic simulation (heating after energy
minimization):
md, warm belly to 300K
&cntrl
imin = 0, irest = 0, ntx = 1,
nstlim = 20000, dt = .002,
ntpr=100, ntwx=5000,
ntt = 1, tempi=10.0, temp0 = 300.0, tautp=1.0,
ntc = 2, ntf = 2,
cut = 999., nsnb=999999, scee = 1.2,
ntb = 0,
ibelly = 1, ntr = 1,
&end
&ewald
eedmeth=4,
&end
-- restraint = belly
5.0
RES a z
END
END
-- belly
RES a z
END
END
-----
Best regards,
Oliver
--
_______________________________________________________________
Oliver Hucke, Dr.
Health Sciences Building - K418C
University of Washington 1959 NE Pacific St.
Dept. of Biochemistry phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email: ohucke.u.washington.edu
_______________________________________________________________
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Received on Wed May 12 2004 - 20:53:01 PDT
